This series of files compile all analyses done during Chapter 2:

All analyses have been done with R 3.6.3.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

Sources of activity considered for the analyses:

Fisheries data considered for the analyses (expressed as number of fishing events or kilograms of collected individuals for each gear):

Gear Code Years Events Species
Trap TrapFish 2010-2015 1061 Buccinum sp., Cancer irroratus, Chionoecetes opilio, Homarus americanus
Bottom-trawl TrawFish 2013-2014 2 Pandalus borealis
Net NetFish 2010 5 Clupea harengus, Gadus morhua
Dredge DredFish 2010-2014 21 Mactromeris polynyma

1. Explorations

1.1. Relationships between parameters

This section explores relationships between human activity exposure indices (dependant variables) and biotic and abiotic parameters (predictors).

Fist, we can compute the Spearman’s correlation coefficients.

Correlation coefficients between habitat parameters and metals concentrations
  om gravel sand silt clay arsenic cadmium chromium copper iron manganese mercury lead zinc S N H J aquaculture city dredging_collect dredging_dump industry shipping_mooring shipping_traffic sewers_rain sewers_waste wharves_city wharves_industry fisheries_trap fisheries_trawl fisheries_net fisheries_dredge cumulative_influence
om 1 -0.379 -0.708 0.68 0.023 0.57 0.486 0.606 0.593 0.586 0.568 0.537 0.587 0.605 -0.026 -0.121 0.122 0.136 -0.41 -0.033 0.22 0.43 0.309 0.518 0.291 0.239 0.401 -0.073 0.366 -0.508 -0.213 0.004 -0.238 0.274
gravel -0.379 1 0.186 -0.471 0.099 -0.127 -0.23 -0.194 -0.23 -0.232 -0.199 -0.207 -0.169 -0.235 0.029 0.007 0.012 0.07 0.143 -0.068 -0.175 -0.161 -0.081 -0.216 -0.02 0 -0.073 -0.061 -0.166 0.16 0.172 -0.055 0.068 -0.12
sand -0.708 0.186 1 -0.788 -0.308 -0.648 -0.504 -0.587 -0.483 -0.407 -0.524 -0.611 -0.588 -0.529 0.059 0.084 0.031 -0.027 0.433 0.279 -0.002 -0.17 -0.102 -0.42 -0.169 -0.31 -0.468 0.324 -0.17 0.428 0.087 -0.158 0.246 -0.058
silt 0.68 -0.471 -0.788 1 0.05 0.548 0.482 0.506 0.441 0.362 0.449 0.566 0.519 0.493 -0.054 -0.013 -0.068 -0.055 -0.409 -0.15 0.046 0.179 0.079 0.424 0.083 0.247 0.391 -0.196 0.175 -0.385 -0.18 0.119 -0.241 0.076
clay 0.023 0.099 -0.308 0.05 1 0.208 0.095 0.129 0.11 0.062 0.144 0.052 0.15 0.107 -0.098 -0.076 -0.044 0.02 -0.059 -0.02 0.025 0.015 0.02 0.006 0.012 0.241 0.238 -0.031 0.037 -0.096 -0.104 0.191 -0.046 0.066
arsenic 0.57 -0.127 -0.648 0.548 0.208 1 0.797 0.862 0.791 0.656 0.78 0.707 0.902 0.87 -0.266 -0.149 -0.193 0.008 -0.657 -0.067 0.06 0.216 0.076 0.66 0.214 0.522 0.709 -0.158 0.213 -0.444 -0.237 0.078 -0.466 0.181
cadmium 0.486 -0.23 -0.504 0.482 0.095 0.797 1 0.818 0.694 0.564 0.717 0.75 0.886 0.853 -0.308 -0.042 -0.291 -0.133 -0.783 -0.015 -0.002 0.186 -0.084 0.728 0.039 0.468 0.701 -0.14 0.142 -0.345 -0.306 -0.001 -0.46 0.111
chromium 0.606 -0.194 -0.587 0.506 0.129 0.862 0.818 1 0.909 0.818 0.917 0.753 0.92 0.939 -0.331 -0.167 -0.273 -0.041 -0.73 -0.02 0.263 0.437 0.103 0.733 0.344 0.596 0.763 -0.103 0.409 -0.323 -0.349 0.055 -0.559 0.362
copper 0.593 -0.23 -0.483 0.441 0.11 0.791 0.694 0.909 1 0.808 0.842 0.715 0.872 0.952 -0.298 -0.172 -0.225 -0.025 -0.655 0.238 0.438 0.571 0.219 0.752 0.432 0.641 0.755 0.169 0.536 -0.319 -0.451 0.033 -0.602 0.553
iron 0.586 -0.232 -0.407 0.362 0.062 0.656 0.564 0.818 0.808 1 0.878 0.461 0.664 0.785 -0.377 -0.273 -0.251 0.034 -0.616 0.114 0.508 0.652 0.325 0.671 0.624 0.578 0.674 0.061 0.644 -0.292 -0.368 0.055 -0.648 0.596
manganese 0.568 -0.199 -0.524 0.449 0.144 0.78 0.717 0.917 0.842 0.878 1 0.658 0.798 0.846 -0.287 -0.096 -0.261 -0.085 -0.758 -0.02 0.422 0.557 0.209 0.769 0.497 0.671 0.822 -0.082 0.562 -0.301 -0.466 0.106 -0.649 0.493
mercury 0.537 -0.207 -0.611 0.566 0.052 0.707 0.75 0.753 0.715 0.461 0.658 1 0.845 0.755 -0.234 -0.084 -0.199 -0.075 -0.724 -0.064 0.053 0.237 -0.043 0.731 0.133 0.509 0.703 -0.142 0.196 -0.356 -0.314 0.01 -0.42 0.168
lead 0.587 -0.169 -0.588 0.519 0.15 0.902 0.886 0.92 0.872 0.664 0.798 0.845 1 0.939 -0.304 -0.135 -0.252 -0.051 -0.707 0.029 0.129 0.316 0.05 0.739 0.211 0.599 0.769 -0.065 0.277 -0.376 -0.307 0.036 -0.475 0.275
zinc 0.605 -0.235 -0.529 0.493 0.107 0.87 0.853 0.939 0.952 0.785 0.846 0.755 0.939 1 -0.32 -0.145 -0.253 -0.056 -0.718 0.152 0.307 0.471 0.151 0.791 0.341 0.603 0.764 0.067 0.429 -0.359 -0.397 0.026 -0.578 0.431
S -0.026 0.029 0.059 -0.054 -0.098 -0.266 -0.308 -0.331 -0.298 -0.377 -0.287 -0.234 -0.304 -0.32 1 0.561 0.705 -0.052 0.348 -0.141 -0.113 -0.158 0.077 -0.255 -0.045 -0.315 -0.33 -0.069 -0.151 0.079 0.217 -0.112 0.335 -0.164
N -0.121 0.007 0.084 -0.013 -0.076 -0.149 -0.042 -0.167 -0.172 -0.273 -0.096 -0.084 -0.135 -0.145 0.561 1 -0.041 -0.683 -0.005 -0.061 -0.139 -0.163 -0.169 -0.023 -0.111 -0.116 -0.067 -0.061 -0.169 0.183 -0.008 -0.137 0.029 -0.133
H 0.122 0.012 0.031 -0.068 -0.044 -0.193 -0.291 -0.273 -0.225 -0.251 -0.261 -0.199 -0.252 -0.253 0.705 -0.041 1 0.598 0.373 -0.087 0.026 -0.014 0.285 -0.243 -0.028 -0.306 -0.328 -0.004 -0.015 -0.058 0.163 -0.035 0.425 -0.089
J 0.136 0.07 -0.027 -0.055 0.02 0.008 -0.133 -0.041 -0.025 0.034 -0.085 -0.075 -0.051 -0.056 -0.052 -0.683 0.598 1 0.186 0.01 0.073 0.054 0.236 -0.128 -0.021 -0.105 -0.146 0.034 0.061 -0.168 0.033 0.127 0.23 -0.014
aquaculture -0.41 0.143 0.433 -0.409 -0.059 -0.657 -0.783 -0.73 -0.655 -0.616 -0.758 -0.724 -0.707 -0.718 0.348 -0.005 0.373 0.186 1 -0.069 -0.168 -0.306 0.128 -0.827 -0.183 -0.597 -0.839 0.079 -0.271 0.282 0.594 0.02 0.722 -0.233
city -0.033 -0.068 0.279 -0.15 -0.02 -0.067 -0.015 -0.02 0.238 0.114 -0.02 -0.064 0.029 0.152 -0.141 -0.061 -0.087 0.01 -0.069 1 0.292 0.369 0.051 0.299 0.133 0.324 0.162 0.969 0.255 -0.097 -0.401 -0.012 -0.424 0.564
dredging_collect 0.22 -0.175 -0.002 0.046 0.025 0.06 -0.002 0.263 0.438 0.508 0.422 0.053 0.129 0.307 -0.113 -0.139 0.026 0.073 -0.168 0.292 1 0.895 0.734 0.359 0.741 0.485 0.416 0.371 0.946 0.012 -0.507 0.028 -0.366 0.849
dredging_dump 0.43 -0.161 -0.17 0.179 0.015 0.216 0.186 0.437 0.571 0.652 0.557 0.237 0.316 0.471 -0.158 -0.163 -0.014 0.054 -0.306 0.369 0.895 1 0.723 0.588 0.805 0.545 0.521 0.436 0.956 -0.173 -0.465 -0.048 -0.518 0.924
industry 0.309 -0.081 -0.102 0.079 0.02 0.076 -0.084 0.103 0.219 0.325 0.209 -0.043 0.05 0.151 0.077 -0.169 0.285 0.236 0.128 0.051 0.734 0.723 1 0.183 0.656 0.17 0.146 0.17 0.765 -0.172 -0.09 -0.086 -0.041 0.61
shipping_mooring 0.518 -0.216 -0.42 0.424 0.006 0.66 0.728 0.733 0.752 0.671 0.769 0.731 0.739 0.791 -0.255 -0.023 -0.243 -0.128 -0.827 0.299 0.359 0.588 0.183 1 0.41 0.592 0.766 0.24 0.5 -0.417 -0.597 -0.05 -0.728 0.543
shipping_traffic 0.291 -0.02 -0.169 0.083 0.012 0.214 0.039 0.344 0.432 0.624 0.497 0.133 0.211 0.341 -0.045 -0.111 -0.028 -0.021 -0.183 0.133 0.741 0.805 0.656 0.41 1 0.568 0.451 0.232 0.834 -0.005 -0.181 0.097 -0.521 0.825
sewers_rain 0.239 0 -0.31 0.247 0.241 0.522 0.468 0.596 0.641 0.578 0.671 0.509 0.599 0.603 -0.315 -0.116 -0.306 -0.105 -0.597 0.324 0.485 0.545 0.17 0.592 0.568 1 0.892 0.279 0.571 -0.07 -0.509 0.209 -0.747 0.661
sewers_waste 0.401 -0.073 -0.468 0.391 0.238 0.709 0.701 0.763 0.755 0.674 0.822 0.703 0.769 0.764 -0.33 -0.067 -0.328 -0.146 -0.839 0.162 0.416 0.521 0.146 0.766 0.451 0.892 1 0.069 0.523 -0.257 -0.569 0.061 -0.75 0.522
wharves_city -0.073 -0.061 0.324 -0.196 -0.031 -0.158 -0.14 -0.103 0.169 0.061 -0.082 -0.142 -0.065 0.067 -0.069 -0.061 -0.004 0.034 0.079 0.969 0.371 0.436 0.17 0.24 0.232 0.279 0.069 1 0.331 -0.042 -0.34 0.016 -0.35 0.632
wharves_industry 0.366 -0.166 -0.17 0.175 0.037 0.213 0.142 0.409 0.536 0.644 0.562 0.196 0.277 0.429 -0.151 -0.169 -0.015 0.061 -0.271 0.255 0.946 0.956 0.765 0.5 0.834 0.571 0.523 0.331 1 -0.094 -0.454 0.037 -0.497 0.9
fisheries_trap -0.508 0.16 0.428 -0.385 -0.096 -0.444 -0.345 -0.323 -0.319 -0.292 -0.301 -0.356 -0.376 -0.359 0.079 0.183 -0.058 -0.168 0.282 -0.097 0.012 -0.173 -0.172 -0.417 -0.005 -0.07 -0.257 -0.042 -0.094 1 0.226 0.132 0.145 -0.075
fisheries_trawl -0.213 0.172 0.087 -0.18 -0.104 -0.237 -0.306 -0.349 -0.451 -0.368 -0.466 -0.314 -0.307 -0.397 0.217 -0.008 0.163 0.033 0.594 -0.401 -0.507 -0.465 -0.09 -0.597 -0.181 -0.509 -0.569 -0.34 -0.454 0.226 1 -0.071 0.513 -0.458
fisheries_net 0.004 -0.055 -0.158 0.119 0.191 0.078 -0.001 0.055 0.033 0.055 0.106 0.01 0.036 0.026 -0.112 -0.137 -0.035 0.127 0.02 -0.012 0.028 -0.048 -0.086 -0.05 0.097 0.209 0.061 0.016 0.037 0.132 -0.071 1 -0.08 0.077
fisheries_dredge -0.238 0.068 0.246 -0.241 -0.046 -0.466 -0.46 -0.559 -0.602 -0.648 -0.649 -0.42 -0.475 -0.578 0.335 0.029 0.425 0.23 0.722 -0.424 -0.366 -0.518 -0.041 -0.728 -0.521 -0.747 -0.75 -0.35 -0.497 0.145 0.513 -0.08 1 -0.617
cumulative_influence 0.274 -0.12 -0.058 0.076 0.066 0.181 0.111 0.362 0.553 0.596 0.493 0.168 0.275 0.431 -0.164 -0.133 -0.089 -0.014 -0.233 0.564 0.849 0.924 0.61 0.543 0.825 0.661 0.522 0.632 0.9 -0.075 -0.458 0.077 -0.617 1

Several types of models were considered to explore relationships between variables: linear, quadratic, exponential and logarithmic. The model with the highest \(R^{2}\) is presented on each plot. Only linear models were implemented, as there are some bugs with the calculation of the others.

AquaInf

CityInf

InduInf

CollDred

DumpDred

MoorShip

TrafShip

RainSew

WastSew

CityWha

InduWha

TrapFish

TrawFish

NetFish

DredFish

Cumulative Influence

1.2. Species abundances by cumulative influence index

Let’s have a look at the distribution of species phyla along the gradient of cumulative influence.

Phylum mean abundances by group
Phylum low bad moderate high good
Annelida NA 29.5 32.3 19.7 NA
Arthropoda NA 20.3 50.6 26.3 NA
Cnidaria NA 0.1 0 0 NA
Echinodermata NA 13.5 1.32 5.12 NA
Mollusca NA 10.8 13.5 15.9 NA
Nematoda NA 22.7 9.95 0.0625 NA
Nemertea NA 0 0.195 0 NA
Sipuncula NA 0 0.268 0.438 NA

2. Species Distribution Models

The aim is to obtain models to predict the structure of benthic communities.

We will use abiotic parameters and the indices of influence (calculated in Section 1) as predictors, and we tested different methods: GLMs, GAMs, Random Forest and HMSC. Each method has been developed in dedicated scripts, whose final objects were imported here to present results and trends.

For each method, results are presented with a table, with McFadden’s R2 and variables coefficients, and maps, with the probability of presence of each taxon for which McFadden’s R2 is higher than 0.2 (and different than 1). The raster presents the results of the SDM (grey: low probability, dark blue: high). Stations are either plotted with colors (green = taxa present, red = taxon absent) or with circles (wider circcles = higher taxon density).

2.1. Generalized Linear Models

Presence/absence data

Here, we considered presence/absence data with a binomial distribution.

Abiotic parameters

McFadden’s R2, match ratios and variables coefficients for each taxon
  R2 MATCHED ERRORS intercept gravel sand silt clay arsenic cadmium chromium copper iron manganese mercury lead zinc
aceroides_aceroides_latipes 0.21 0 % 31.8 % -128 -27.7 70 70.8 -555 0.0222 0.417 0.811 1.02 -0.763 -0.448 0.622 -1.46 -0.428
akanthophoreus_gracilis 0.35 0 % 45.5 % -8.11 -11.2 -23 -22.4 -48.6 3.84 0.949 1.59 2.29 -1.55 -1.26 1.53 -5.86 -2.8
ameritella_agilis 0.41 0 % 13.6 % -311 41.7 84.3 84.9 -1605 -0.181 2.96 6.95 -0.786 -2.91 -8.14 -2.32 -6.38 2.79
ameroculodes_edwardsi 0.35 0 % 9.1 % -276 -104 -213 -215 -1588 -3.55 0.342 4.22 -0.327 0.169 -7.51 0.128 -2.52 0.215
ampelisca_vadorum 1 0 % 4.5 % -69.8 -969 -1975 -2013 -1160 14 -43 137 -40.7 4.24 -65.9 11.7 42.8 -72.9
amphipoda 0.18 13.6 % 50 % -0.616 67.1 136 138 79.5 0.431 0.257 1.97 -0.872 -0.694 -0.981 0.735 0.461 -0.875
anonyx_lilljeborgi 0.35 0 % 9.1 % -4.15 147 299 305 173 -3.88 -2.29 5.45 -5.56 -0.579 -0.526 0.39 0.803 2.29
anthozoa 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
arcteobia_anticostiensis 1 0 % 4.5 % -66.3 1191 2449 2501 1419 31 32.5 -33.8 50.9 -4.05 8.28 20.4 -11.8 -105
arrhoges_occidentalis 1 0 % 0 % -68 -3125 -6317 -6459 -3653 18.1 -21 69 -63.9 -18.3 2.17 -14.9 -13.6 30.4
astarte_sp 0.38 0 % 4.5 % -315 -119 -240 -246 -1830 -0.337 -2.35 -0.622 -2.42 -1.19 1.07 0.117 -0.987 4.95
axinopsida_orbiculata 0.16 0 % 18.2 % -369 -40.2 -81.5 -82.7 -2049 0.171 0.541 -0.206 0.381 0.0898 -0.58 -1.81 1.11 -1.1
axiothella_catenata 1 0 % 4.5 % -74.2 1818 3681 3753 2127 -4.01 -53.9 -35.2 7.29 10.7 -28 15.3 130 -41.4
bathymedon_longimanus 1 0 % 13.6 % -1676 20832 42940 43977 25020 832 859 -1385 158 154 -856 -338 -423 -315
bathymedon_obtusifrons 1 0 % 9.1 % -106 5106 10357 10571 5964 4.63 44.4 88.3 46.9 -157 5.05 -37.6 -1.73 -45
bipalponephtys_neotena 0.27 86.4 % 13.6 % 2.3 55.2 111 115 64.6 0.101 0.201 -2.59 0.41 0.0756 0.484 1.89 -1.56 1.53
boreochiton_ruber 0.32 0 % 4.5 % -283 -43.6 -89.5 -90.8 -1557 -9.67 -4.54 -0.0512 -7.21 -0.499 2.78 -2.19 6.2 6.65
brachydiastylis_sp 0.61 0 % 18.2 % -26 203 408 418 192 1.95 9.27 22.8 2.45 1.9 -26.1 4.21 -32.3 -0.0727
byblis_gaimardii 0.35 0 % 0 % -265 -51.5 -105 -107 -1465 -7.38 -3.75 5.42 -6.4 -0.975 -0.986 0.228 1.84 3.88
cancer_irroratus 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
caprella_septentrionalis 0.57 0 % 13.6 % -16.1 -63.5 -131 -136 -73.3 -15 6.36 -4.7 13.5 -10.3 1.47 -9.79 9.96 -5
chaetodermatida 0.26 0 % 31.8 % -336 38.6 79.5 81.5 -1768 -3.64 -0.829 -1.6 -0.837 -0.178 0.0666 -0.159 0.585 2.64
chionoecetes_opilio 1 0 % 22.7 % -445 3273 6586 6925 2638 35.6 -357 -206 -709 21.3 151 64.5 -199 978
chlamys_islandica 1 0 % 4.5 % -328 -36162 -73416 -74849 -42397 -104 -50.2 126 212 29.7 -62.6 -94.6 111 -196
chone_sp 1 0 % 4.5 % -239 147 658 594 392 84.7 254 -89.3 628 -42.4 -115 48.8 4.59 -688
ciliatocardium_ciliatum 1 0 % 4.5 % -471 -4290 -8584 -9082 -4945 157 -288 187 152 17.7 -388 109 242 -170
cirripedia 1 0 % 4.5 % -35.2 364 733 749 425 1.04 2.01 -7.87 -22.9 -0.673 17.3 -5.41 -23.9 41.3
cistenides_granulata 0.27 0 % 22.7 % -325 48.3 98 100 -1705 -0.631 -1.91 2.38 -4.38 -0.263 -0.417 0.304 -0.299 2.86
cossura_longocirrata 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
crassicorophium_bonellii 0.51 0 % 0 % -236 33.3 68.3 69.1 -1212 1.54 1.35 1.44 5.4 -2.14 2.45 -3.63 0.731 -9.62
crenella_decussata -2.31 0 % 9.1 % -2.37e+15 2.16e+16 4.34e+16 4.33e+16 2.52e+16 5.02e+14 1.12e+15 2.42e+15 2.48e+15 -5.67e+14 -1.32e+15 6.91e+14 -2.7e+15 -3.7e+15
cumacea 0 0 % 9.1 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
cyclocardia_borealis 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
cyrtodaria_siliqua 1 0 % 9.1 % -185 1725 3638 3710 2147 -11.2 -141 -361 -280 3.6 217 -134 112 505
diastylis_rathkei 0.31 0 % 4.5 % -4.08 -151 -308 -313 -178 -3.54 -2.75 3.82 -0.165 0.145 0.0639 -2.17 4.93 -3.7
diastylis_sculpta 0.31 0 % 4.5 % -3.99 48.2 99.1 102 57.3 -3.31 -0.763 2.38 1.65 -2.06 1.07 -2.09 -0.521 -0.0184
diastylis_sp 1 0 % 13.6 % -1145 8399 16669 17706 9314 -1984 -249 371 -866 211 -99.2 33.8 168 844
echinarachnius_parma 0.56 4.5 % 13.6 % -10.4 -90.2 -182 -186 -103 -8.86 -0.445 1.25 -3.94 0.267 -3.94 -1.31 -3.87 6.86
edotia_montosa 1 0 % 9.1 % -144 -435 -851 -948 -489 32.5 31.6 -95.7 34.9 -30.7 33.2 -35.6 -83.6 135
ennucula_tenuis 0.48 22.7 % 50 % -2.76 116 234 241 123 3.27 0.375 -1.22 3.9 0.0848 -3.54 4.01 -6.49 -2.32
eteone_sp -6.59 0 % 13.6 % -3.79e+15 -1.48e+17 -3.01e+17 -3.07e+17 -1.74e+17 2.86e+14 -7.48e+14 1.24e+15 -1.72e+14 -2.13e+14 -2.08e+14 -7.52e+14 6.35e+14 -5.83e+14
euchone_sp 1 0 % 4.5 % -106 5106 10357 10571 5964 4.63 44.4 88.3 46.9 -157 5.05 -37.6 -1.73 -45
eudorella_emarginata 0.49 0 % 18.2 % -139 121 240 249 -579 0.73 3.66 3.37 3.62 1.06 -3.26 2.04 -7.8 -1.76
eudorellopsis_integra 0.37 40.9 % 50 % 1.37 -34.7 -70.3 -70.6 -40.5 2.37 -0.755 0.00696 -1.5 -0.8 0.96 3.02 -5.25 3.67
euspira_pallida -5.62 0 % 4.5 % -2.18e+15 -5.74e+16 -1.17e+17 -1.19e+17 -6.91e+16 -2.94e+14 -1.22e+15 -1.2e+15 -1.87e+15 -1.43e+13 1.04e+15 -8.97e+14 1.07e+15 2.6e+15
glycera_capitata 1 0 % 13.6 % -81.3 -2635 -5386 -5503 -3102 -5.81 51 -68.9 108 12.5 -22 -21.3 -5.76 -41.3
glycera_sp 0.46 0 % 4.5 % -6.98 -61.4 -125 -127 -73.1 -3.16 0.61 5.41 -1.63 -9.63 2.69 -1.07 0.904 2.62
goniada_maculata 0.31 22.7 % 45.5 % -342 47 96.5 100 -1808 1.11 0.579 1.58 -1.4 0.38 -2.89 1.38 -2.93 0.558
guernea_prinassus_nordenskioldi 1 0 % 27.3 % -401 1879 3669 3899 2012 255 339 488 222 84.1 -707 127 -1148 95.8
halacaridae_spp 1 0 % 4.5 % -328 -36162 -73416 -74849 -42397 -104 -50.2 126 212 29.7 -62.6 -94.6 111 -196
haminoea_solitaria 0.39 0 % 4.5 % -39.6 -57.1 18.7 18.8 -9.96 8.61 12.8 11.3 29.2 -0.911 -20.7 -8.26 -3.7 -43.3
hardametopa_carinata 1 0 % 4.5 % -106 5106 10357 10571 5964 4.63 44.4 88.3 46.9 -157 5.05 -37.6 -1.73 -45
harmothoe_sp 0.32 0 % 9.1 % -235 -104 -215 -217 -1377 -0.508 0.613 0.36 2.87 -0.109 0.462 -3.53 -1.15 -0.974
harpacticoida 0.13 13.6 % 40.9 % -0.0838 35.2 72.1 72.6 41.2 0.549 1.91 1.42 3.88 -0.0578 -1.46 0.424 -1.33 -4.79
hediste_diversicolor 0.38 0 % 22.7 % -2.8 240 487 496 281 -0.789 2.9 -0.709 5.18 -0.126 0.644 -0.451 2.8 -8.77
heteranomia_squamula 1 0 % 4.5 % -55.2 1487 3007 3065 1740 1.34 -11.3 -91.4 -32.1 1.2 45.3 -21.1 25.5 70
hiatella_arctica -5.68 0 % 4.5 % -2.19e+15 -3.41e+16 -6.94e+16 -7.08e+16 -3.99e+16 -3.45e+14 -1.24e+15 -3.11e+15 -2.33e+15 -1.98e+14 1.57e+15 -1.35e+15 1.4e+15 3.88e+15
holothuroidea 0.73 0 % 4.5 % -46.4 -232 -267 -277 -158 -23.2 -9.22 -15.4 -9.09 -7.14 16.3 -10.9 15.5 24.4
idotea_phosphorea 0.64 0 % 4.5 % -318 -306 -625 -639 -1989 -24.6 -3.08 -16.6 -6.49 2.17 10 -11.8 36 2.24
ischyroceridae_spp 1 0 % 9.1 % -106 5774 11718 11977 6788 8.87 -85.1 46.3 56 6.9 -56.5 27.9 -16 -9.85
ischyrocerus_anguipes 1 0 % 0 % -991 -37963 -77196 -79039 -44579 -697 395 68.5 680 -724 130 -246 260 -206
isopoda 1 0 % 4.5 % -379 -3392 -5693 -5836 -3253 -257 -155 -267 -292 -91.8 261 -189 284 445
lacuna_vincta 1 0 % 4.5 % -69.2 -1912 -3880 -3967 -2236 -23.9 -9.84 -64.8 -17.7 -2.41 45.3 -20.8 41.7 23
lamprops_fuscatus 0.33 0 % 18.2 % -335 -54.5 -109 -112 -1867 -5.71 0.515 0.241 3.08 0.13 1.25 -0.177 1.46 -4.24
lamprops_quadriplicata 1 0 % 0 % -65.1 -933 -1855 -1922 -1079 25.6 26.4 40.4 49.6 -4.96 -2.48 9.43 26.1 -150
lepeta_caeca 0.43 0 % 4.5 % -349 -311 -633 -645 -2237 -6.4 -0.65 -1.34 0.364 0.225 0.561 -2.72 5.91 -0.94
leucon_leucon_nasicoides 0.12 31.8 % 40.9 % -0.541 -2.28 -4.64 -4.22 -2.25 0.396 -0.441 1.18 -0.84 0.101 -0.898 1.04 -0.0168 -0.417
littorina_littorea 0.56 0 % 4.5 % -340 -43.9 -87.9 -89.4 -1861 -11.5 -2.66 -7.59 -4.56 0.271 4.31 -7.21 14.1 6.32
lumbrineridae_spp -1.77 0 % 4.5 % -1.82e+15 3.57e+16 7.25e+16 7.41e+16 4.24e+16 1.54e+14 2.09e+14 1.09e+15 -2.15e+15 -1.49e+14 5.9e+14 -5.76e+14 1.47e+15 -9.55e+14
lysianassidae_spp 1 0 % 9.1 % -43.3 -371 -753 -769 -434 4.36 -5.12 13 2.64 -5.56 12 -7.91 -54.6 39.2
macoma_calcarea 0.27 77.3 % 22.7 % 380 -20.6 -42 -41.8 2043 1.62 2.49 0.917 4.54 -0.0867 -0.987 0.559 -3.82 -5.77
maera_danae 1 0 % 4.5 % -239 147 658 594 392 84.7 254 -89.3 628 -42.4 -115 48.8 4.59 -688
maldane_sarsi 0.52 0 % 4.5 % -19.1 -30.4 4.1 8.95 -2.06 -1.05 -2.12 5.34 4.58 0.162 -1.28 -7.1 4.13 -7.22
maldanidae_spp 0.24 4.5 % 50 % -13.6 -93.6 -103 -104 -58.7 -0.00423 0.359 1.93 1.96 0.0238 -1.43 0.467 -2.45 -1.33
monoculopsis_longicornis -4.67 0 % 4.5 % -1.5e+15 -2.67e+16 -5.28e+16 -5.38e+16 -3.11e+16 -2.99e+13 -4.25e+14 -3.35e+14 -4.49e+14 -6.85e+14 4.7e+14 2.92e+14 -1.11e+15 1.91e+15
muculus_musculus_discors 1 0 % 4.5 % -328 -36162 -73416 -74849 -42397 -104 -50.2 126 212 29.7 -62.6 -94.6 111 -196
mytilus_sp 0.39 0 % 9.1 % -5.1 -11.3 -22.8 -22.2 -14.9 -4.61 -0.182 -1.21 8.14 -0.715 -0.123 -6.05 10.1 -12
nematoda 0.46 18.2 % 27.3 % -6.81 158 321 326 150 0.642 -2.12 0.0525 -4.13 -2.96 1.96 -0.133 -0.402 4.89
nemertea 1 0 % 0 % -86.5 -2609 -5329 -5453 -3071 -7.09 55.7 -27.7 79.7 17.9 -59.5 22.3 -44.2 -27.5
neoleanira_tetragona 1 0 % 0 % -54 -474 -893 -934 -522 18.1 25.6 35.2 49.9 -2.33 -18.9 10.7 19.5 -124
nephtyidae_spp 0.3 0 % 9.1 % -148 -148 -174 -178 -796 1.1 -0.596 3.92 -2.4 -6.99 2.04 -0.574 0.053 1.83
nephtys_caeca 0.67 0 % 4.5 % -239 385 780 792 -809 4.69 12 11.8 11.8 1.88 -9.78 0.28 -14.7 -16.3
nephtys_incisa 0.24 4.5 % 40.9 % -1.68 9.16 17.2 19.2 7.02 0.506 -1.36 0.819 0.0401 -0.131 -1.83 1.16 -1.19 0.436
nephtys_sp 0.27 0 % 13.6 % -92.2 -26.3 49.9 52.8 -363 -0.574 -1.32 1.43 -2.4 0.159 -2.25 -0.137 -1.98 3.1
nuculana_minuta 0.14 0 % 18.2 % -326 41.2 82.7 85.3 -1718 0.12 0.118 -0.326 0.778 -0.182 -0.325 0.272 -0.394 -1.49
nymphonidae_spp 1 0 % 4.5 % -55.2 1487 3007 3065 1740 1.34 -11.3 -91.4 -32.1 1.2 45.3 -21.1 25.5 70
oenopota_sp 0.26 0 % 4.5 % -3.68 92.2 187 191 107 1 2.13 -2.22 6.8 -0.773 1.16 -0.869 -0.663 -8.16
oligochaeta 0.36 0 % 36.4 % -14.7 -171 -262 -267 -150 0.451 1.55 4.39 3.31 -0.286 -2.47 1.32 -2.99 -4.13
ophelia_limacina 0.16 0 % 4.5 % -319 -47.4 -97.5 -98.9 -1779 0.568 0.63 2.49 2.09 0.0654 -2.77 0.78 -2.18 -2.2
opheliidae_spp -2.79 0 % 0 % -1.81e+15 -5.92e+16 -1.21e+17 -1.23e+17 -7.02e+16 -2.95e+14 -3.93e+14 1.38e+15 -7.25e+14 -2.15e+14 -6.13e+14 -3.75e+13 9.02e+14 -8.8e+14
ophiopholis_aculeata 1 0 % 0 % -685 -40703 -82785 -84083 -48261 -158 105 598 228 70 -440 -358 -335 -251
ophiura_robusta 0.4 0 % 4.5 % -318 66.7 136 137 -1625 -3.45 -3.08 -0.715 -3.64 -0.516 1.82 -1.69 3.66 3.59
orchomenella_minuta 0.42 0 % 0 % -259 -152 -308 -313 -1564 -0.888 -0.276 -2.2 2.26 -2.28 2.53 -2.03 -1.48 1.22
ostracoda 0.33 4.5 % 45.5 % -2.09 -66.7 -134 -136 -79.5 1.05 -0.258 -1.56 2.14 -2.6 -0.298 0.422 -2.76 1.74
pagurus_sp 1 0 % 4.5 % -66.3 1191 2449 2501 1419 31 32.5 -33.8 50.9 -4.05 8.28 20.4 -11.8 -105
pagurus_pubescens 0.51 0 % 0 % -266 111 225 226 -1252 -8.95 -1.35 0.803 1.36 0.53 -6.05 0.399 3.38 -0.142
pandalus_montagui 1 0 % 4.5 % -50.7 405 822 843 478 10.7 25.5 23.2 66 -4.58 0.174 24.3 -68.6 -77.5
parathyasira_equalis 0.39 0 % 4.5 % -39.6 -57.1 18.7 18.8 -9.96 8.61 12.8 11.3 29.2 -0.911 -20.7 -8.26 -3.7 -43.3
parvicardium_pinnulatum 0.28 0 % 9.1 % -7.46 58.7 119 122 69 1.78 4.12 6.42 10.6 -0.821 -8.41 -4.72 -0.863 -14.9
periploma_leanum 0.3 0 % 4.5 % -147 96.5 260 267 -573 -0.166 2.53 -2.05 4 -0.285 -0.864 0.576 -0.0542 -2.57
philine_lima 1 0 % 4.5 % -66.3 1191 2449 2501 1419 31 32.5 -33.8 50.9 -4.05 8.28 20.4 -11.8 -105
philomedes_sp 0.35 0 % 9.1 % -263 15.2 30.1 30.4 -1387 2.65 1.91 7.17 0.389 0.167 -6.72 1.02 -8.76 -0.747
pholoe_longa 1 0 % 4.5 % -106 5106 10357 10571 5964 4.63 44.4 88.3 46.9 -157 5.05 -37.6 -1.73 -45
pholoe_sp 0.27 18.2 % 54.5 % -0.494 12.8 25.6 27 12.5 -1.86 -1.26 -4.23 0.104 -0.676 2.82 -0.774 -0.25 4.17
phoxocephalus_holbolli 0.37 0 % 18.2 % -3.43 -22.4 -45 -46.2 -26.1 -8.54 -5.45 -2.94 -12.4 -3.38 5.83 -4.24 6.99 18
polynoidae_spp 0.18 0 % 50 % -1.31 -23.9 -48.4 -48.1 -27.1 -0.581 -1.14 0.835 -2.46 -0.329 0.15 0.149 -0.455 2.17
pontogeneia_inermis 1 0 % 4.5 % -58.7 -1849 -3760 -3833 -2171 15.2 18.6 101 56.1 5.66 -63.7 14.6 -28.9 -108
pontoporeia_femorata 0.47 9.1 % 50 % -1.96 -96.7 -197 -200 -113 -0.623 2.45 -2.17 4.45 0.768 0.0189 1.45 -1.57 -2.08
praxillella_praetermissa 0.41 0 % 18.2 % -13.7 197 464 474 263 0.0526 3.63 -5.13 7.54 0.327 1.17 -0.826 -0.291 -5.58
propebela_turricula 0.24 0 % 9.1 % -132 123 348 356 -426 -0.303 -1.82 0.496 -0.834 -0.21 -1.01 0.0246 3.56 -1.42
protomedeia_fasciata 0.27 0 % 4.5 % -339 22.8 46.2 47.5 -1806 -1.88 -0.599 2.71 -3.68 -0.0173 0.191 0.571 1.73 0.127
protomedeia_grandimana 0.17 27.3 % 40.9 % -0.449 55.5 112 115 65.1 0.151 0.502 1.47 3.78 -0.175 -1.52 0.59 -0.388 -4.57
puncturella_noachina 1 0 % 13.6 % -81.3 -2635 -5386 -5503 -3102 -5.81 51 -68.9 108 12.5 -22 -21.3 -5.76 -41.3
quasimelita_formosa 0.26 0 % 40.9 % -3.83 3.8 6.81 8.67 -7.43 0.181 0.512 3.25 3.79 0.164 -3.93 -0.507 0.307 -5.75
quasimelita_quadrispinosa 1 0 % 9.1 % -106 5774 11718 11977 6788 8.87 -85.1 46.3 56 6.9 -56.5 27.9 -16 -9.85
retusa_obtusa 0.55 0 % 9.1 % -12 -145 -272 -278 -157 2.76 7.92 7.9 14.1 0.641 -2.95 2.43 -15.9 -9.98
sabellidae_spp 0.3 0 % 9.1 % -128 -69.7 -35.1 -36.1 -624 -0.0248 1.6 1.73 0.236 -1.01 0.585 0.281 -2.42 -0.0749
scoletoma_fragilis 0.47 0 % 13.6 % -14.7 6.85 79.5 83.6 44.4 -2.53 1.75 1.51 7.19 -0.607 2 -3.35 0.519 -8.66
scoletoma_sp 1 0 % 9.1 % -328 -36162 -73416 -74849 -42397 -104 -50.2 126 212 29.7 -62.6 -94.6 111 -196
scoloplos_sp 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
serripes_groenlandicus 1 0 % 4.5 % -114 -11234 -22826 -23279 -13186 4.31 34.3 -57.1 107 23 -7.18 21.4 -13.9 -36.4
sipuncula 0.28 4.5 % 27.3 % -13.3 118 313 322 180 0.476 0.171 -0.743 0.254 -0.935 -0.409 0.106 -1.66 1.36
solamen_glandula 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
solariella_sp 0.63 0 % 13.6 % -11.3 -63 -131 -128 -78.6 -9.06 -12 1.16 -18.6 -1.08 2.33 -1.15 -0.643 22.6
strongylocentrotus_sp -6.59 0 % 4.5 % -3.79e+15 -1.48e+17 -3.01e+17 -3.07e+17 -1.74e+17 2.86e+14 -7.48e+14 1.24e+15 -1.72e+14 -2.13e+14 -2.08e+14 -7.52e+14 6.35e+14 -5.83e+14
tachyrhynchus_erosus 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
thracia_septentrionalis 0.23 0 % 27.3 % -2.38 93 188 192 109 -1.98 0.114 -3.35 -0.844 -1.14 2.71 -2.27 1.66 2.89
thyasira_gouldi 0.14 4.5 % 45.5 % -1.06 30.5 61.6 63.5 36.2 0.0633 -0.706 0.506 -0.85 -1 -0.0117 0.546 -1.9 2.08
thyasira_sp 0 0 % 4.5 % -26.6 -4.41e-13 -9.09e-13 -9.1e-13 -5.18e-13 1.22e-14 -5.17e-15 1.06e-14 -4.56e-14 1.63e-15 -1.1e-14 2.62e-14 -5.77e-14 5.65e-14
trichotropis_bicarinata 0.52 0 % 18.2 % -76.7 324 666 682 367 43 66.6 114 44.8 11.6 -153 15 -166 -37.4
turritellopsis_stimpsoni 0.56 0 % 0 % -321 -155 -314 -323 -1883 2.22 -5.07 7.21 3.61 -5.21 -6.56 0.645 4.94 -5.86
yoldia_myalis 0.31 0 % 4.5 % -311 -58.9 -120 -124 -1722 -4.54 0.0538 1.58 1.07 0.226 -3.44 -0.0334 1.63 -1.53

Prediction of specific richness based on this model:

Influence indices

McFadden’s R2, match ratios and variables coefficients for each taxon
  R2 MATCHED ERRORS intercept city dredging_collect dredging_dump industry shipping_mooring shipping_traffic sewers_rain sewers_waste wharves_city wharves_industry fisheries_trap fisheries_trawl fisheries_net fisheries_dredge
aceroides_aceroides_latipes 0.14 0 % 31.8 % -1.99 -1.66 0.414 0.757 0.362 -0.789 1.04 -3.52 3.76 2.69 -2.98 0.214 -0.534 -1.09 -0.0996
akanthophoreus_gracilis 0.47 13.6 % 27.3 % -3.32 1.32 -0.289 -7.74 5.28 -0.419 3.56 -8.77 8.15 -0.00491 1.8 0.424 -0.222 -0.739 1.31
ameritella_agilis 0.59 0 % 13.6 % -9.82 15.7 12.3 28.7 -9.46 5.03 0.852 9.09 -23.4 -23.5 -29.2 0.0366 0.574 -0.102 -1.02
ameroculodes_edwardsi -9.4 0 % 0 % -2.84e+15 9.93e+14 -8.99e+14 -9.48e+14 1.61e+15 -1.95e+15 8.76e+14 -2.45e+15 2.73e+15 6.77e+14 1.69e+13 4.48e+13 5.61e+13 4.48e+14 1.05e+13
ampelisca_vadorum 1 0 % 4.5 % -43.8 -13.2 4.6 0.927 -11.6 -14 16.4 -36.1 41.4 16.9 -9.81 -39.3 0.559 2.72 -0.735
amphipoda 0.19 13.6 % 36.4 % -1.02 2.15 0.788 4.39 1.63 0.101 0.33 0.361 0.436 -2.74 -7.17 0.257 -0.346 -1.26 -0.0973
anonyx_lilljeborgi 0.45 0 % 22.7 % -5.22 -9.38 -7.93 4.74 -5.55 -4.12 0.881 0.354 -2.13 7.25 6.54 -0.0854 -6.59 -1.74 -5.51
anthozoa 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
arcteobia_anticostiensis 1 0 % 4.5 % -130 -138 -223 -71.8 -45.6 -57.2 -37.2 -53 105 188 310 -155 -73.1 6.45 34.9
arrhoges_occidentalis 1 0 % 4.5 % -62 -43.9 14.1 80.5 6.74 -63.7 -4.97 -125 164 52.2 -95.9 0.597 1.34 13.8 -24.5
astarte_sp -10.34 0 % 4.5 % -1.66e+15 3.96e+15 2.33e+15 9.78e+14 7.45e+14 1.33e+15 3.57e+14 3.2e+15 -4.37e+15 -4.59e+15 -3.52e+15 -2.01e+14 -7.46e+14 4.33e+13 2.46e+14
axinopsida_orbiculata 0.24 4.5 % 22.7 % -2.5 7.52 -1.61 2.89 2.03 1.29 1.44 -1.86 -0.722 -6.59 -3.06 0.601 0.634 -0.743 0.737
axiothella_catenata 1 0 % 13.6 % -399 -739 -480 -202 257 -119 105 -845 910 1211 106 0.642 20.2 93 70.5
bathymedon_longimanus 1 0 % 22.7 % -174 129 -364 -411 206 -50.3 -57 -65.7 151 25.3 554 43.4 -118 14.4 48.8
bathymedon_obtusifrons 1 0 % 13.6 % -96.5 -403 -37.9 -27.5 35.8 -59.6 -113 -17.8 207 427 -39.8 -8.24 8.32 1.69 -4.72
bipalponephtys_neotena 0.34 68.2 % 27.3 % 2.53 0.994 1.98 2.61 3.39 0.749 1.59 -3.33 5.12 -0.125 -9 1.4 -0.284 1.78 1.81
boreochiton_ruber 1 0 % 9.1 % -352 574 183 329 -352 416 85 587 -1442 -957 68.5 24.6 24 19.9 -4.85
brachydiastylis_sp 1 0 % 9.1 % -65.3 -89.8 98.2 126 -45.1 18.6 -16 78.2 -76.5 28.9 -192 -31.3 2.98 -0.774 -5.37
byblis_gaimardii 1 0 % 4.5 % -112 -17.5 8.95 -24.7 -24.6 -23.9 66.6 -19.1 36.3 23.5 -28.9 -247 -3.8 3.58 38.6
cancer_irroratus 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
caprella_septentrionalis 0.49 0 % 9.1 % -172 -4.3 -10.2 -2.77 -0.86 -2.42 -3.28 10.8 -18 13.6 5.41 -0.506 -251 -2.21 -289
chaetodermatida 0.52 0 % 31.8 % -29.9 -89.6 10.1 -5.02 5.11 6.19 8.57 9.63 -24.1 95 -20.7 0.0288 -2.07 -0.969 0.81
chionoecetes_opilio 1 0 % 9.1 % -400 812 55.3 1411 123 -141 328 449 -712 -1100 -1578 58.4 -506 26.5 -334
chlamys_islandica 1 0 % 0 % -27.9 1.42 3.89 -1.98 0.0843 1.87 -3.99 -4.43 4.9 0.168 2.89 -0.524 8.04 0.931 0.159
chone_sp 1 0 % 4.5 % -60.6 -179 -23.4 -58.1 50.8 -32.3 -50 -5.97 113 208 -16.6 6.96 1.67 -0.0546 1.03
ciliatocardium_ciliatum 1 0 % 4.5 % -62.7 32.9 -36.4 173 4.35 -41.1 16.4 -23 17.8 -42.5 -129 0.0246 -18.6 8.87 -34.7
cirripedia 1 0 % 4.5 % -51.1 40.8 29.1 -18 39.5 22.5 -1.74 53.9 -50.2 -75.4 -52.8 18.4 -11.6 -0.658 -0.756
cistenides_granulata 0.35 4.5 % 27.3 % -4.9 -19 0.0479 -7.73 -1.01 9.87 1.52 2.45 -12.3 14.7 7.9 0.523 0.326 -1.57 0.417
cossura_longocirrata 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
crassicorophium_bonellii 1 0 % 4.5 % -91.3 -110 13.5 56.2 -72.6 -93.9 -39.2 -44.9 91.5 94.2 41.8 -65.6 9.83 6.85 -1.83
crenella_decussata 1 4.5 % 9.1 % -348 153 251 -30.1 -125 535 240 521 -1331 -538 -87.4 -40 -114 -2.04 -111
cumacea 0 0 % 9.1 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
cyclocardia_borealis 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
cyrtodaria_siliqua 1 0 % 0 % -126 541 -114 89.4 43.4 63.2 95.1 85.5 -253 -578 41.1 -15 -11.9 17.3 34.1
diastylis_rathkei 0.57 0 % 13.6 % -12.2 -0.0937 7.82 31.8 -19.1 -14.1 -3.9 12.3 -18 -10.1 -6.29 -5.1 0.824 -1.07 -4.51
diastylis_sculpta 0.46 0 % 9.1 % -24.8 23.4 2.79 27.8 -10.1 6.27 -46.7 3.97 -24.4 -27.6 39.6 0.209 -3.25 4.84 -1.62
diastylis_sp 1 0 % 0 % -104 39.1 -139 246 45.3 -19.8 -112 118 -94.9 -58.9 -34.9 2.22 13 10.9 -75.7
echinarachnius_parma 0.67 13.6 % 18.2 % -12.6 -16 2.06 -17.9 -9.09 8.51 -1.24 9.91 -29.5 15.2 23.9 0.838 0.629 -1.59 -3.37
edotia_montosa 0.41 0 % 18.2 % -140 -8.59 -7.46 -8.14 -1.8 -7.34 2.1 -6.21 8.85 10.8 12.5 -7.38 -170 -2.52 -276
ennucula_tenuis 0.46 27.3 % 36.4 % -1.57 -9.53 2.93 -5.67 2.77 3.75 3.19 -3.5 0.831 9.76 -1.25 -1.14 -0.0617 1.76 3.5
eteone_sp 1 0 % 13.6 % -43.6 -19.5 -6.38 -3.41 -14.4 -19.8 8.99 -50.5 61.9 27.9 14.7 -28.8 9.5 4.05 2.01
euchone_sp 1 0 % 9.1 % -96.5 -403 -37.9 -27.5 35.8 -59.6 -113 -17.8 207 427 -39.8 -8.24 8.32 1.69 -4.72
eudorella_emarginata -19.05 9.1 % 9.1 % -2.95e+15 4.59e+13 1.69e+14 1.15e+15 9.72e+14 1.49e+15 8.19e+14 -2.89e+15 3.04e+15 -6.64e+14 -2.78e+15 -8.63e+13 5.52e+14 5.9e+14 2.16e+14
eudorellopsis_integra 0.72 50 % 13.6 % -3.72 -72.5 14.1 -9.24 7.17 24.1 6.06 -6.02 -4.91 62.8 -17.2 0.55 -0.475 -1.66 2.84
euspira_pallida 1 0 % 4.5 % -214 520 178 719 92.2 -175 86.9 -195 179 -482 -828 -31.1 8.34 64.1 -0.805
glycera_capitata 1 0 % 4.5 % -63.9 186 77.3 -0.33 48.5 59.4 56.4 63.3 -107 -209 -144 8.59 -0.11 2.35 2.91
glycera_sp 1 0 % 9.1 % -645 -219 -94.9 1712 -866 290 -882 991 -1426 -419 -7.91 -167 166 73.3 60.1
goniada_maculata 0.34 27.3 % 27.3 % -4.1 -22.7 1.29 -1.75 1.33 9.53 1.67 -3.61 -5.84 18.9 0.141 0.52 0.68 2.17 -0.0196
guernea_prinassus_nordenskioldi 1 0 % 18.2 % -57.7 73.6 34.7 -30.2 76.3 44.8 -36.7 92.5 -89.1 -92.5 -52.7 18.2 2.03 1.06 0.618
halacaridae_spp 1 0 % 0 % -27.9 1.42 3.89 -1.98 0.0843 1.87 -3.99 -4.43 4.9 0.168 2.89 -0.524 8.04 0.931 0.159
haminoea_solitaria 1 0 % 13.6 % -140 313 -456 -280 107 -118 -5.62 -272 305 -219 722 50.3 9.45 32.9 58.4
hardametopa_carinata 1 0 % 9.1 % -96.5 -403 -37.9 -27.5 35.8 -59.6 -113 -17.8 207 427 -39.8 -8.24 8.32 1.69 -4.72
harmothoe_sp 1 0 % 4.5 % -63.4 186 77.3 -0.33 48.5 59.4 56.4 63.3 -107 -209 -144 8.59 -0.11 7.46 2.91
harpacticoida 0.21 18.2 % 40.9 % 0.0137 -1.15 0.615 0.00311 -1 -0.957 0.623 -3.56 4.11 2.45 -0.703 0.812 -0.0265 -1.32 0.0844
hediste_diversicolor 0.54 0 % 18.2 % -124 1.81 10.7 11.3 -2.72 -1.72 -1.92 5.32 -6.05 -5.61 -14.2 -0.475 -17.7 -2.3 -354
heteranomia_squamula 1 0 % 4.5 % -199 587 -147 139 102 123 -224 184 -332 -595 288 18 -28.4 39.4 46
hiatella_arctica -10.14 0 % 4.5 % -1.85e+15 1.88e+15 -1.84e+15 -3.69e+14 6.1e+14 -6.5e+14 -2.23e+14 4.87e+14 -8.66e+14 -1.62e+15 1.97e+15 1.82e+14 -9.71e+14 1.7e+14 -1.12e+14
holothuroidea -3.46 0 % 0 % -1.94e+15 4.3e+15 5.66e+14 -2.06e+15 2.67e+14 2.1e+14 1.18e+15 -6.16e+14 -3.17e+14 -3.96e+15 1.48e+15 -3.09e+14 1.53e+14 2.37e+14 4.42e+14
idotea_phosphorea -6.59 0 % 4.5 % -2.9e+15 7.36e+14 -1.15e+15 1.89e+15 -1.18e+15 -5.34e+14 -5.99e+14 1.44e+15 -2.32e+15 -6.92e+14 6.35e+14 -4.54e+14 -2.47e+14 2.48e+14 1.81e+13
ischyroceridae_spp 1 0 % 9.1 % -121 -1.31 106 253 -75.6 60.3 47.9 -146 -11.6 -45.2 -242 -0.702 24.6 30.9 -17.4
ischyrocerus_anguipes -12.23 0 % 4.5 % -2.12e+15 -6.4e+14 1.55e+15 1.37e+15 -1.61e+15 8.62e+14 -5.93e+13 1.09e+15 -3.08e+15 8.43e+13 -2.14e+15 1.62e+14 -5.57e+14 1.45e+14 -9.24e+14
isopoda 1 0 % 0 % -29.3 12.4 -15.5 -3.66 -0.848 2.92 3.18 1.97 -1.08 -10.1 18.4 1.11 1.33 0.261 10
lacuna_vincta 1 0 % 31.8 % -98.2 203 29.3 -142 109 27.4 80.8 38.2 -64.6 -213 -57.9 39 -78.4 0.768 -15.3
lamprops_fuscatus 0.36 0 % 31.8 % -8.56 -0.574 -0.793 1.28 -3.57 -2.48 1.89 -0.966 -0.511 0.127 2.93 -0.431 -21.6 -1.44 0.457
lamprops_quadriplicata -6.59 0 % 0 % -2.02e+15 -3.17e+15 1.6e+15 2.08e+15 1.45e+14 8.42e+14 -1.04e+15 8.75e+14 1.95e+14 2.44e+15 -3.86e+15 -1.24e+14 2.08e+14 1.71e+14 -4.28e+14
lepeta_caeca 1 0 % 13.6 % -455 1033 346 296 -301 371 94.3 1041 -1869 -1225 -323 -47.6 0.588 -0.465 -10.1
leucon_leucon_nasicoides 0.4 22.7 % 45.5 % -5.13 -33 6.44 1.58 1.31 17.3 1.84 12.2 -24.5 22.3 -9.18 -0.569 -1.86 0.957 0.132
littorina_littorea -7.91 0 % 9.1 % -1.98e+15 8.75e+14 7.51e+14 -2.47e+15 1.4e+14 3.67e+14 4.76e+13 1.74e+15 -2.34e+15 2.14e+13 3.45e+14 -4.32e+13 -8.94e+14 -1.84e+13 -5.07e+14
lumbrineridae_spp -7.31 0 % 0 % -2.18e+15 -7.48e+14 -1.05e+15 -1.2e+15 1.18e+15 7.67e+14 -1.81e+15 -2.7e+14 6.79e+13 7.86e+14 2.74e+15 3.53e+14 1.87e+14 3.47e+14 -2.29e+14
lysianassidae_spp 1 0 % 4.5 % -79.2 218 -0.248 -180 49.6 1.74 69.4 -50 19.2 -201 129 -14.3 0.439 5.97 6.8
macoma_calcarea 0.18 63.6 % 27.3 % 1.66 1.59 5.44 3.13 0.703 1.29 0.56 0.657 -1.69 -2.12 -8.71 -0.326 0.254 1.51 0.61
maera_danae 1 0 % 4.5 % -60.6 -179 -23.4 -58.1 50.8 -32.3 -50 -5.97 113 208 -16.6 6.96 1.67 -0.0546 1.03
maldane_sarsi 1 0 % 4.5 % -76.4 -86.5 -302 -33.7 16.5 -90 -24.4 -32.4 135 157 291 -3.22 -8.62 6.68 2.76
maldanidae_spp 0.25 13.6 % 27.3 % -3.31 -12.1 0.723 -1.26 -0.227 4.06 -0.463 0.92 -3.37 10.3 0.983 -2.8 -0.451 -1.4 -0.169
monoculopsis_longicornis 1 0 % 4.5 % -628 815 618 479 610 -578 611 -754 1274 -110 -2026 -167 86.6 123 177
muculus_musculus_discors 1 0 % 0 % -27.9 1.42 3.89 -1.98 0.0843 1.87 -3.99 -4.43 4.9 0.168 2.89 -0.524 8.04 0.931 0.159
mytilus_sp 0.34 0 % 27.3 % -4.52 -1.69 -2.42 4.63 -3.17 -3.84 -3.03 7.82 -7.33 1.78 4.08 -0.369 0.0943 -1.73 -0.0446
nematoda 0.32 27.3 % 27.3 % -0.262 1.66 3.44 -0.907 1.17 0.015 2.13 1.43 -1.47 -1.86 -6.09 -0.0353 -0.884 1.33 0.228
nemertea -14.18 0 % 4.5 % -1.52e+15 -6.46e+14 1.21e+14 3.56e+14 1.44e+15 -1.33e+14 5.77e+14 -1.44e+15 1.84e+15 9.94e+14 -2.72e+15 8.63e+13 -2.43e+14 2.55e+14 -5.54e+14
neoleanira_tetragona 1 0 % 0 % -261 172 502 793 -41.1 337 -285 558 -728 -420 -969 15.1 72.3 32.8 -3.36
nephtyidae_spp 0.33 0 % 13.6 % -4.82 6.96 5.33 0.562 3.71 3.37 -1.13 5.94 -6.8 -9.98 -7.8 -3.09 1.3 -1.19 0.339
nephtys_caeca 0.41 0 % 4.5 % -5.58 2.19 -0.98 6.49 -5.69 0.622 -1.04 0.598 -7.97 -4.79 2.36 0.532 -0.023 -0.969 -7.37
nephtys_incisa 0.36 13.6 % 22.7 % -6.18 -30.8 6.63 -1.16 2.73 15 2.11 6.51 -18.2 22.5 -7.19 -1.63 -0.264 -1.51 -0.294
nephtys_sp 1 0 % 4.5 % -110 5.37 90.1 330 20.2 12.8 -119 271 -279 -103 -307 -8.34 0.474 -0.405 -140
nuculana_minuta 0.44 4.5 % 31.8 % -6.61 -9.54 5.17 -7.5 6.02 9.1 4.67 6.12 -12.3 4.9 -7.94 1.16 -3.05 1.52 0.0729
nymphonidae_spp 1 0 % 4.5 % -199 587 -147 139 102 123 -224 184 -332 -595 288 18 -28.4 39.4 46
oenopota_sp 0.28 0 % 9.1 % -3.86 7.08 -1.58 -0.741 3.69 0.211 -2.82 1.27 -0.334 -5.5 2.85 0.287 0.262 -0.935 1.2
oligochaeta 0.53 0 % 36.4 % -24.9 -18.6 -4.25 3.55 -7.27 -5.24 13.7 -21.5 23 19.4 -6.61 0.413 -17.6 -1.26 -45.5
ophelia_limacina 0.58 0 % 9.1 % -24.1 -36.6 0.892 -8.07 -0.729 8.57 1.71 -3.12 -7.74 33.6 3.4 -1.43 -1.19 -1.31 -51.4
opheliidae_spp 1 0 % 13.6 % -357 -805 -912 -432 173 -835 -140 -1124 1773 1328 1056 -236 24.4 76.1 -159
ophiopholis_aculeata 1 0 % 0 % -1093 1743 1229 1455 632 1076 -115 1785 -2623 -2604 -2926 -1356 18.2 95.9 -204
ophiura_robusta 1 0 % 13.6 % -346 521 220 207 -206 350 -6.95 769 -1450 -896 20.2 -43.1 -3.94 -6.25 -256
orchomenella_minuta 1 0 % 27.3 % -133 154 174 -227 70.9 78.2 93.4 108 -129 -160 -119 33.3 -37.9 -7.93 -81.5
ostracoda 0.33 0 % 50 % -1.64 0.641 3.92 -1.08 1.97 0.827 1.72 0.137 -0.148 0.418 -6.58 -0.857 -0.618 -1.35 1.73
pagurus_sp 1 0 % 4.5 % -130 -138 -223 -71.8 -45.6 -57.2 -37.2 -53 105 188 310 -155 -73.1 6.45 34.9
pagurus_pubescens 1 0 % 18.2 % -257 108 186 -161 47.9 494 190 342 -931 -394 -36.2 -38.9 -75.5 4.6 1.9
pandalus_montagui 1 0 % 4.5 % -130 287 127 307 -26.5 -69.7 105 171 -225 -378 -370 -76.6 -69.1 1.83 0.562
parathyasira_equalis 1 0 % 13.6 % -140 313 -456 -280 107 -118 -5.62 -272 305 -219 722 50.3 9.45 32.9 58.4
parvicardium_pinnulatum 1 0 % 18.2 % -563 -656 -1364 -898 1.56 -246 -308 155 -147 1304 1879 -41 -100 2.49 -336
periploma_leanum -6.59 0 % 4.5 % -2.56e+15 1.87e+15 9.23e+14 3.39e+14 -7.55e+13 3.28e+15 6.18e+14 6.71e+14 -3.18e+15 -2.52e+15 -2.28e+14 2.49e+13 1.87e+14 3.34e+14 4.14e+14
philine_lima 1 0 % 4.5 % -130 -138 -223 -71.8 -45.6 -57.2 -37.2 -53 105 188 310 -155 -73.1 6.45 34.9
philomedes_sp 1 0 % 9.1 % -359 -1047 -109 -31.7 182 -96.9 209 -581 616 1217 -234 -178 -45.6 53.9 33.5
pholoe_longa 1 0 % 9.1 % -96.5 -403 -37.9 -27.5 35.8 -59.6 -113 -17.8 207 427 -39.8 -8.24 8.32 1.69 -4.72
pholoe_sp 0.32 13.6 % 54.5 % -0.459 5.3 4.58 5.98 -0.652 2.15 1.18 6.3 -9.74 -7.87 -8.66 0.0837 -1.26 -1.68 0.621
phoxocephalus_holbolli 0.45 0 % 27.3 % -3.75 11.1 3.21 8.78 -3.56 -1.23 2.44 7.79 -12.2 -15.4 -7.04 0.931 -5.57 1.5 -0.165
polynoidae_spp 0.08 0 % 36.4 % -1.47 1.15 1.36 2.03 -0.137 1.39 0.157 1.93 -3.4 -2.47 -3.18 -0.372 -0.607 -1.41 -0.228
pontogeneia_inermis 1 0 % 4.5 % -128 -218 -104 -116 44.7 -178 -16.8 -237 405 354 120 -169 6.43 17.1 4.2
pontoporeia_femorata 0.48 9.1 % 40.9 % -13.3 2.6 -12.1 -1.85 -5.81 3.4 4.09 -3.06 4.23 -1.54 15.6 0.518 -5.75 -1.67 -14.3
praxillella_praetermissa 0.42 4.5 % 9.1 % -16.7 2.63 -13.9 6.29 2.32 -1.3 -2.22 4.36 -2.83 -3.04 9.1 -0.19 -45.4 -1.11 2.29
propebela_turricula 1 0 % 22.7 % -453 -879 -421 -540 514 -205 -39.1 -887 1282 1276 75.8 83.4 31.5 99.4 53.2
protomedeia_fasciata 0.27 0 % 4.5 % -3.24 -4.58 -0.534 6.5 -2.24 -0.663 -0.286 -0.724 1.1 2.79 -3.26 -0.0172 0.282 -1.17 0.664
protomedeia_grandimana 0.12 18.2 % 40.9 % -0.677 -0.735 -0.323 3.32 0.342 -0.061 -0.302 0.762 -0.237 0.641 -2.79 -0.148 -0.0372 -1.41 0.0936
puncturella_noachina 1 0 % 4.5 % -63.9 186 77.3 -0.33 48.5 59.4 56.4 63.3 -107 -209 -144 8.59 -0.11 2.35 2.91
quasimelita_formosa 0.4 4.5 % 45.5 % -5.55 -11.9 -4.63 -7.68 1.44 -4.13 -0.291 0.084 5.48 17.1 5.87 -11.4 -0.835 1.47 -0.138
quasimelita_quadrispinosa 1 0 % 9.1 % -121 -1.31 106 253 -75.6 60.3 47.9 -146 -11.6 -45.2 -242 -0.702 24.6 30.9 -17.4
retusa_obtusa -8.45 0 % 9.1 % -1.71e+15 -3.9e+15 7.53e+14 2.69e+15 -7.58e+14 -7.58e+14 -6.99e+14 8.41e+14 -7.99e+14 2.68e+15 -1.46e+15 3.7e+14 -3.02e+14 7.56e+13 -8.81e+14
sabellidae_spp 0.37 0 % 18.2 % -5.14 7.18 -0.464 3.69 3.54 0.949 3.06 -0.253 -1.55 -10 -8.63 1.91 -5.18 -1.06 -3.52
scoletoma_fragilis -10.88 0 % 22.7 % -1.55e+15 -2.68e+15 1.14e+15 4.75e+15 -1.61e+15 7.7e+14 -1.63e+15 2.86e+15 -3.28e+15 7.74e+14 -2.53e+15 -3.36e+13 -1.45e+14 5.52e+13 -4.57e+14
scoletoma_sp 1 0 % 4.5 % -27.9 1.42 3.89 -1.98 0.0843 1.87 -3.99 -4.43 4.9 0.168 2.89 -0.524 8.04 0.931 0.159
scoloplos_sp 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
serripes_groenlandicus 1 0 % 13.6 % -517 436 -432 136 81.3 93.3 -683 -333 486 -194 1088 -0.607 233 136 161
sipuncula 0.25 4.5 % 22.7 % -3.01 -2.52 -0.644 -2.17 2.73 1.2 -0.648 2.56 -1.97 2.06 0.0856 -0.632 -1.06 -1.59 -1.26
solamen_glandula 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
solariella_sp 0.45 0 % 9.1 % -27 -94.7 10.7 -5.61 -10.3 14.2 2.3 14.8 -42.3 79.2 12 -0.461 1.86 -1.52 -1.17
strongylocentrotus_sp 1 0 % 4.5 % -43.6 -19.5 -6.38 -3.41 -14.4 -19.8 8.99 -50.5 61.9 27.9 14.7 -28.8 9.5 4.05 2.01
tachyrhynchus_erosus 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
thracia_septentrionalis 0.25 0 % 27.3 % -2.72 6.44 -0.789 2.72 -1.22 -0.308 -0.213 3.55 -6.32 -8.04 0.893 0.328 -0.615 -1.49 -2.8
thyasira_gouldi 0.3 4.5 % 31.8 % -4.25 -13.3 4.86 -2.76 2.23 10.9 2.81 3.13 -12.1 8.38 -4.5 -1.08 -0.312 -1.3 1.24
thyasira_sp 0 0 % 4.5 % -26.6 -1.15e-14 -1.77e-15 -4.6e-15 1.9e-15 -6.55e-15 -8.13e-15 9.56e-15 5.52e-16 1.04e-14 7.91e-15 -3.06e-17 1.76e-15 -2.85e-15 9.03e-16
trichotropis_bicarinata 1 0 % 4.5 % -93.6 245 13.1 68.3 88.1 9.71 -25.9 -21.9 -6.77 -205 -73.7 -4.1 0.72 21.1 9.22
turritellopsis_stimpsoni 1 0 % 0 % -820 2858 602 962 -185 111 405 946 -2137 -3488 -708 -576 -4.67 86 -9.2
yoldia_myalis 1 0 % 13.6 % -126 526 45.9 6.63 60.3 77.3 157 157 -337 -610 -119 -36.8 -90.8 3.26 8.69

Prediction of specific richness based on this model:

Density data

Here, we considered density data with a Poisson distribution.

Abiotic parameters

Influence indices

2.2. Hierarchical Modelling of Species Communities

First, we initiate the HMSC model with the chosen data, priors and parameters.

HMSC_model <- hmsc(HMSC_data, HMSC_param, HMSC_prior, family = "overPoisson", niter = 100000, nburn = 1000, thin = 100)

Here are the diagnostics to evaluate each model’s quality.

Human activities

Trace plots

Explanatory power

Confidence intervals

Variance partitioning

Habitat parameters

Trace plots

Explanatory power

Confidence intervals

Variance partitioning

All variables

Trace plots

Explanatory power

Confidence intervals

Variance partitioning

Finally, we can predict the values of our parameters within BSI.

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